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The Path of Messenger RNA Through the Ribosome. THIS FILE, 1JGO, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, AND MRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY
1JGO

Structural Similarities for the Entities in PDB 1JGO

The following structural similarities have been found using the jFATCAT-rigid algorithm [1,2]. To reduce the number of hits, a 40% sequence identity clustering has been applied and a representative chain taken from each cluster. If the representative chain consists of multiple domains, each domain is included in the search. If available, the SCOP 1.75 domain assignment [3] is used. Otherwise algorithmic domain assignments are computed using the ProteinDomainParser [4].

Entity #1: Chains: A
Description: 30S 16S ribosomal RNA rna
Length: 1522

This entity is not a polypeptide entity and therefore cannot be considered for the all vs. all structure alignments.

 



Entity #10: Chains: J
Description: 30S RIBOSOMAL PROTEIN S7 protein
Length: 156
No structure alignment results are available for 1JGO.J explicitly.

It is represented by chain 1RSS.A which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1RSS.A

 
 
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Entity #11: Chains: K
Description: 30S RIBOSOMAL PROTEIN S8 protein
Length: 138
No structure alignment results are available for 1JGO.K explicitly.

It is represented by chain 1SEI.A which has more than 90% sequence identity.

 Click here to show the structure comparison results for representative 1SEI.A

 
 
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Entity #12: Chains: L
Description: 30S RIBOSOMAL PROTEIN S9 protein
Length: 128
No structure alignment results are available for 1JGO.L explicitly.

It is represented by chain XXXX.null which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #13: Chains: M
Description: 30S RIBOSOMAL PROTEIN S10 protein
Length: 105
No structure alignment results are available for 1JGO.M explicitly.

It is represented by chain 3D3B.J which has more than 50% sequence identity.

 Click here to show the structure comparison results for representative 3D3B.J

 
 
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Entity #14: Chains: N
Description: 30S RIBOSOMAL PROTEIN S11 protein
Length: 129
No structure alignment results are available for 1JGO.N explicitly.

It is represented by chain 4CVN.E which has more than 40% sequence identity.

 Click here to show the structure comparison results for representative 4CVN.E

 
 
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Entity #15: Chains: O
Description: 30S RIBOSOMAL PROTEIN S12 protein
Length: 135
No structure alignment results are available for 1JGO.O explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #16: Chains: P
Description: 30S RIBOSOMAL PROTEIN S13 protein
Length: 126
No structure alignment results are available for 1JGO.P explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #17: Chains: Q
Description: 30S RIBOSOMAL PROTEIN S14 protein
Length: 61
No structure alignment results are available for 1JGO.Q explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #18: Chains: R
Description: 30S RIBOSOMAL PROTEIN S15 protein
Length: 89
No structure alignment results are available for 1JGO.R explicitly.

It is represented by chain 4A5U.B which has more than 50% sequence identity.

 Click here to show the structure comparison results for representative 4A5U.B

 
 
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Entity #19: Chains: S
Description: 30S RIBOSOMAL PROTEIN S16 protein
Length: 91
No structure alignment results are available for 1JGO.S explicitly.

It is represented by chain XXXX.null which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #2: Chains: B,C
Description: tRNA(Phe) rna
Length: 76

This entity is not a polypeptide entity and therefore cannot be considered for the all vs. all structure alignments.

 



Entity #20: Chains: T
Description: 30S RIBOSOMAL PROTEIN S17 protein
Length: 105
No structure alignment results are available for 1JGO.T explicitly.

It is represented by chain XXXX.null which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #21: Chains: U
Description: 30S RIBOSOMAL PROTEIN S18 protein
Length: 88
No structure alignment results are available for 1JGO.U explicitly.

It is represented by chain XXXX.null which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #22: Chains: V
Description: 30S RIBOSOMAL PROTEIN S19 protein
Length: 93
No structure alignment results are available for 1JGO.V explicitly.

It is represented by chain 3A1P.B which is 100% sequence identical.

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Entity #23: Chains: W
Description: 30S RIBOSOMAL PROTEIN S20 protein
Length: 106
No structure alignment results are available for 1JGO.W explicitly.

It is represented by chain XXXX.null which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #24: Chains: X
Description: 30S RIBOSOMAL PROTEIN THX protein
Length: 26
No structure alignment results are available for 1JGO.X explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #3: Chains: D
Description: tRNA(Phe) rna
Length: 74

This entity is not a polypeptide entity and therefore cannot be considered for the all vs. all structure alignments.

 



Entity #4: Chains: 1
Description: MESSENGER RNA MK27 rna
Length: 27

This entity is not a polypeptide entity and therefore cannot be considered for the all vs. all structure alignments.

 



Entity #5: Chains: E
Description: 30S RIBOSOMAL PROTEIN S2 protein
Length: 256
No structure alignment results are available for 1JGO.E explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #6: Chains: F
Description: 30S RIBOSOMAL PROTEIN S3 protein
Length: 239
No structure alignment results are available for 1JGO.F explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #7: Chains: G
Description: 30S RIBOSOMAL PROTEIN S4 protein
Length: 209
No structure alignment results are available for 1JGO.G explicitly.

It is represented by chain XXXX.null which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #8: Chains: H
Description: 30S RIBOSOMAL PROTEIN S5 protein
Length: 162
No structure alignment results are available for 1JGO.H explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

 Click here to show the structure comparison results for representative XXXX.null

 
 
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Entity #9: Chains: I
Description: 30S RIBOSOMAL PROTEIN S6 protein
Length: 101
No structure alignment results are available for 1JGO.I explicitly.

It is represented by chain 1CQM.A which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 1CQM.A

 
 
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To see how chain 1JGO.I compares with the representative chain d1cqma_ select a method below:




  • Update Status Hide
    Feb 24 2015

    Cluster data are up-to-date as of:
     
  • Table Legend Hide
    • Rank: current row position. Changes with different sorting orders and filter rules
    • Domain 2: Domain name of 2nd domain. Can be either a SCOP ID (d<PDB ID><Chain ID><Domain ID>), ProteinDomainParser ID (PDP:<PDB ID><Chain ID><Domain ID>)
    • Title: Protein chain description
    • P-value: P-value of this alignment (FATCAT) (default sorted by this)
    • Score: Raw alignment score (FATCAT)
    • RMSD: RMSD value of the alignment
    • Len1: Domain 1 length
    • Len2: Domain 2 length
    • %ID: % sequence identity in the alignment. A 40% sequence identity filter is applied before the structure alignments are calculated, so most results show low similarity. If the sequences are of vastly different lengths, the clustering procedure will group them in different clusters, even if they share a region of high sequence similarity.
    • %Cov1: The coverage, or %, of aligned residues in chain 1
    • %Cov2: The coverage, or %, of aligned residues in chain 2

    The table is sorting is by P-value by default. Clicking on the column header will change the sort order. Select the Filter Results lense img icon to apply other filtering criteria.

     
Comparison Tool

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Documentation

A detailed description of the procedure for the all vs. all alignments is available.